Examples with Structure de.bioforscher.jstructure.model.structure.Structure used on opensource projects

Example 61 with Structure

use of de.bioforscher.jstructure.model.structure.Structure in project jstructure by JonStargaryen.

the class A02_WriteDatasetCsv method handleProtein.

private static String handleProtein(String pdbId, String chainIds, String thermophile) {
    System.out.println("handling " + thermophile + " protein " + pdbId + " with chains " + chainIds);
    Structure structure = StructureParser.fromPdbId(pdbId).parse();
    List<Chain> chains = chainIds.equals("Null") ? Stream.of(structure.chainsWithAminoAcids().findFirst().get()).collect(Collectors.toList()) : Pattern.compile(",").splitAsStream(chainIds).map(chainId -> {
        Optional<Chain> optionalChain = structure.select().chainId(chainId).asOptionalChain();
        return optionalChain.orElseGet(() -> structure.select().chainId(chainId.toUpperCase()).asChain());
    }).collect(Collectors.toList());
    return chains.stream().map(chain -> handleChain(pdbId, chain, thermophile)).collect(Collectors.joining(System.lineSeparator()));
}